The 49ers are where the Raiders were three years ago – drastically undermanned, in the midst of unrelenting losing, and with Fort Knox-like money under the salary cap. Obviously, the 10-2 Raiders have made the right moves in hiring coach Jack Del Rio, drafting players like Derek Carr and Amari Cooper, and acquiring players like …

On further review, however, San Francisco’s injury-free 2011 season wasn’t lucky. It was the continuation of a trend. In 2010, the 49ers’ defensive starters missed two games due to injury. In 2009, they missed 11. In 2008 … they missed three games. …

After re-signing Ahmad Brooks, Carlos Rogers and Alex Smith while placing the franchise tag on Dashon Goldson, 21 of their 22 projected offensive and defensive starters were on the team in 2011. In addition, most of these guys aren’t going anywhere. Twenty of the 22 projected starters are under contract beyond 2012, with 14 scheduled to stay in San Francisco through 2014. …

Who will win the battle to be the 49ers’ backup quarterback: Colin Kaepernick or Josh Johnson?
Pose the question to Roger Theder and it’s like asking the former Cal head coach and NFL assistant which of his three grown children he loves the most.
A ren… …

A renowned quarterback guru who lives in Orinda, Theder, 72, trained both Kaepernick and Johnson during their high-school careers and has since remained in contact. Johnson, an Oakland native, has returned to the Bay Area and worked with Theder in the summers during his four-year NFL career as a backup with the Bucaaneers. Theder scripted Kaepernick’s drills at Nevada’s pro day prior to last year’s draft. …

As a quarterback who often fell asleep during post-midnight, game-film study sessions in college, Josh Johnson initially bonded with Jim Harbaugh over their shared passion for all things football.
In 2003, during a recruiting visit to Oakland Tech High… …

Holt (6-0, 245), who is projected as a late-round pick or an undrafted free agent, ranked 10th in the Pac-12 in tackles (82) and tackles for loss (10.5) last year. As a junior, he tied for third in the conference with three forced fumbles. Holt was not invited to the NFL combine. …

During Harbaugh’s first recruiting visit to Oakland Tech in 2003, he lined up pencils in front of Johnson that were meant to be defensive fronts. In a July interview with The Chronicle, Johnson said he knew he’d found a kindred spirit. Johnson often fell asleep during late-night, film-study sessions in college. …

(03-22) 23:26 PDT — Former Tampa Bay backup quarterback Josh Johnson often talked about his desire to reunite with his old college coach, Jim Harbaugh, at some point in his NFL career.
As it turns out, that point is now.
After spending his first four… …

Johnson (6-3, 205), who played for 49ers coach Jim Harbaugh for three seasons at the University of San Diego, has made five starts in his four-year career, throwing five touchdowns, 10 interceptions and compiling a 57.7 passer rating. …

At 6-foot-6 and 250 pounds, Fleener’s blend of size and wheels suggests he could join the likes of New England’s Rob Gronkowski (6-6, 265) and New Orleans’ Jimmy Graham (6-6, 260), who overwhelmed defenses in 2011. Gronkowski set NFL single-season records for touchdowns (17) and yards (1,327) by a tight end. Graham’s 1,310 yards rank second all-time. …

Ginn had taken free-agent visits to Detroit, Minnesota and Baltimore and had expressed a desire to be known more as a wide receiver in an interview with the Detroit Free Press. In his two seasons with the 49ers, Ginn, one of the NFL’s top returners, has just 31 catches for 383 yards and one touchdown. …

For starters, let’s begin with the end. Manningham concluded the call by saying, “Thanks for interviewing me.” It was a nice touch. The last time I heard an athlete express such a sentiment, I was covering a high-school softball game, I think. …

Now the Jets have a prayer.
They finalized the trade that sent draft picks to the Denver Broncos for Tim Tebow.
It got complicated for a while, but now Tebow is definitely going to the Jets, pending final approval by the United Nations General Assembly… …

Evidently Alex Smith’s breakout 2011 season didn’t just net him the three-year, $24 million contract he signed Wednesday.
It also gave an unmistakable swagger to the 49ers quarterback who routinely has been described as polite and deferential throughou… …

It didn’t take long for Roger Goodell to realize that the Saints’ Bountygate punishments had to make the Patriots’ Spygate penalties look like an hour of clapping erasers after school. The commissioner hammered the lead perpetrators, handing down a season-long suspension for head coach Sean Payton and an indefinite ban for former defensive coordinator Gregg Williams.

Bill Belichick didn’t miss a game when the league learned in 2007 that the Patriots coach had authorized illicit videotaping of opponents’ defensive signals. He simply had to pay a $500,000 fine while his club forfeited a first-round draft pick. If Goodell had suspended Belichick, he would have had no choice but to ban Payton and Williams for life and completely gut the next two drafts for the Saints, instead of docking them a pair of second-rounders.

Spygate, after all, didn’t come loaded with phrases such as “knockout hits” and “kill shots.” The electronic shenanigans in New England threatened the league’s integrity, but not its very existence.

The widespread belief that Payton would miss only four to six games discounted the repercussions on other fronts, especially in the courtroom. The revelations about the Saints’ bounties came as former players lined up to join lawsuits against the NFL, accusing its leadership of obscuring evidence tying the violence of the sport to brain damage. If Goodell had allowed Payton to coach this year, he might as well have told team owners to start writing huge settlement checks.

The Saints will also lose their general manager’s services for a half-season, and assistant coach Joe Vitt for six games. One has to wonder whether Goodell even considered stripping the Saints of their two-year-old Super Bowl trophy, which they won during the bounty years.

That idea, like all attempts to rewrite history, always appeared to be a non-starter. When players by the dozens responded to the original bounty revelations by citing variations on the scheme elsewhere, or shrugging off the assassin’s mentality as part of the game, it became clear that Bountygate had to focus on the involvement of high-level officials and their cover-up attempts.

When the first reports came out about the bounties, Goodell may have thought the story would fade quickly. The information was released like a trial balloon, set loose on a Friday afternoon, the classic crisis strategy for a corporate or political newsmaker.

The story, it turned out, had the legs of Emmitt Smith. It called for an equally strong response. The punishments came down 19 days after the original announcement, and a little less than 24 hours after Peyton Manning embraced Denver and John Elway. That drama, with all its glorious distractions, had to end before the commissioner could seize a whole news cycle to smack down Payton, Williams and the Saints.

Drew Brees almost immediately turned to his Twitter account to proclaim support for his suspended head coach. “I am speechless. Sean Payton is a great man, coach, and mentor,” the quarterback’s tweet said. “The best there is. I need to hear an explanation for this punishment.”

The NFL had already clearly delineated Payton’s failure of leadership and duplicity during the investigation. If he has any doubts about what happened, he should rent a DVD of “All the President’s Men” and maybe invite Brees over for a showing.

Williams’ departure for St. Louis, at the end of the Saints’ season and six weeks before Bountygate surfaced, added to the pressure to come down hard on Payton. Otherwise, the Rams might have paid more heavily for New Orleans’ sins than the Saints did.

The team just let Williams walk, only three years after Payton had transferred $250,000 of his own paycheck to land the aggressive defensive coordinator. Did the Saints know that they were all about to be busted, and think that splitting up would make sorting out punishments more complicated?

Granted, it wasn’t unusual for Williams to wear out his welcome with a head coach. He apparently alienated Joe Gibbs in Washington by not informing him of a plan to send only 10 men out for the opening play of a game, in honor of slain cornerback Sean Taylor.

But at the time, the move made sense for one, vital reason. Williams’ methods had started to fail. The Saints’ defense faltered badly all year, drafting in the wake of a magnificent offense. The 49ers, rendered helpless by the Saints’ excess aggression in their preseason opener, took full advantage of New Orleans’ predictability and tendency to over-pursue the quarterback when they met in January. As a result, they delivered a knockout blow in the playoffs. No extra payment required.

(03-21) 22:28 PDT — Meting out unprecedented punishment for a crush-for-cash bounty system that targeted key opposing players, the NFL suspended New Orleans Saints head coach Sean Payton without pay for next season and indefinitely banned the team’s … …

“The thing from day one when I first met with coach Harbaugh is that he’s always been up front and he’s always been honest with me. And he’s continued to do that throughout this entire process. That’s one of the reasons that I love playing for him. So, nothing there. Obviously, looking forward to having an offseason with him.” …